ricalc-package: Overview of R/ricalc package

In kbroman/ricalc: Calculations for Recombinant Inbred Lines

Overview of R/ricalc package

Description

A brief introduction to the contents of the R/ricalc package.

Stuff for the gamma model

• coinc.gam: Calculate the three-point coincidence function for the gamma model.

• mf.gam: Map function for the gamma model.

• imf.gam: Inverse of map function for the gamma model.

Data

• mouseL: Estimated genetic lengths of mouse chromosomes.

• threept.AI: Three-point haplotype probabilities for 8-way RIL, autosome, under interference.

• threept.ANI: Three-point haplotype probabilities for 8-way RIL, autosome, with no interference.

• threept.XI: Three-point haplotype probabilities for 8-way RIL, X chromosome, under interference.

• threept.XNI: Three-point haplotype probabilities for 8-way RIL, X chromosome, with no interference.

Symbolic data

• fulltm: Generation-to-generation transition matrices for 2- and 4-way RIL by selfing and by sibling mating (in symbolic notation...lists of lists of character strings).

• mtm: Transition matrices for meiosis, again in symbols...lists of lists of character strings).

Counting and enumerating parental types

• lookup: Lookup tables for parental types in the generation of multiple-strain RIL, representing the

• get.start: Symbolic notation for the starting state in the generation of multiple-strain RIL.

• count.absorb: Count the absorbing states in multiple-strain RIL.

Calculations and simulations

• sim.ri: Simulate multiple-strain RIL.

• get.ril.coinc: Numerical calculation of the 3-point coincidence-type quantity for 2- and 4-way RIL.

• get.ril.prob: Numerical calculation of haplotype probabilities on 2- or 4-way RIL chromosomes.

• get.full.tm: Calculate the generation-to-generation transition matrix for the formation of RIL.

• get.full.tm.symbolic: Calculate the generation-to-generation transition matrix for the formation of RIL, in symbolic form.

• convert.full.tm: Convert a sparse version of a transition matrix into a full matrix.

Author(s)

Karl W Broman, [e-mail]

References

Broman, K. W. (2005) The genomes of recombinant inbred lines. Genetics 169, 1133–1146.

Teuscher, F. and Broman, K. W. (2007) Haplotype probabilities for multiple-strain recombinant inbred lines. Genetics 175, 1267–1274.

kbroman/ricalc documentation built on May 17, 2023, 11:54 p.m.